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Embase: An introduction to indexing 20 October 2014
- 1. Embase: An introduction to indexing Presented by Ann-Marie Roche 22 October 2014 a.roche@elsevier.com Embase® is a registered trademark of Elsevier BV.
- 2. 2 • Webinar control panel: • ‘chat’ for questions or ‘ask a question’ • minimize option for full screen view • Q&A at the end of the webinar • The goal is to understand how indexing works in Embase and how it impacts your search results. NEED TO KNOWS Ann-Marie Roche 22 October 2014 An introduction to indexing
- 3. EMBASE IS AS COMPREHENSIVE AS POSSIBLE 3 0 % 50 % 100 % FEB 2014 | EMBASE SALES PRESENTATION Percentage of relevant articles retrieved Effort / tools required GOOGLE EMBASE PUBMED SOURCE SCOPUS TEXT MINING
- 4. ANATOMY OF AN INDEX 4 Ann-Marie Roche 22 October 2014 An introduction to indexing
- 6. Tables
- 7. EMBASE INDEX 7 Ann-Marie Roche 22 October 2014 An introduction to indexing
- 8. EMBASE INDEX (DRUG SUBHEADINGS) 8 Ann-Marie Roche 22 October 2014 An introduction to indexing
- 9. EMBASE INDEX (DISEASE SUBHEADINGS) 9 Ann-Marie Roche 22 October 2014 An introduction to indexing
- 10. INDEXING NEEDS A THESAURUS 10 Focus on drugs and devices, with dynamic updating Structure Content Updates Drug-rich content • >30,000 drug terms • ALL generics, trade names & chemical names Faceted structure • natural-language • synonym-rich • polyhierarchical Dynamic updating • candidate term source list • updates 3x each year • all terms backposted Medical devices • .> 3,000 device terms (pre-2012: <1000 terms) For further information: http://www.embase.com/info/what-is-embase/emtree Ann-Marie Roche 22 October 2014 An introduction to indexing
- 11. NOT MISSING ANY IMPORTANT INFORMATION 11 Embase Medline Humira 16,200 4048 Enbrel 19,711 4197 Remicade 30,347 9,493 Advair 2425 264 Lantus 6101 1741 Rituxin 40,829 13,076 Avastin 35,591 1,086 FEB 2014 | EMBASE SALES PRESENTATION
- 12. BROWSING EMTREE TO FIND DRUG NAMES 12 Searching for Adverse reactions BROWSE EMTREE FACETS Ann-Marie Roche 22 October 2014 An introduction to indexing
- 13. 13 Searching for Adverse reactions DRUG SEARCH FIND A SPECIFIC DRUG TERM Ann-Marie Roche 22 October 2014 An introduction to indexing
- 14. 14 adverse reactions FIND ADVERSE EVENTS FOR CISPLATIN Ann-Marie Roche 22 October 2014 An introduction to indexing
- 15. FILTER FROM LIST OF INDEXED DISEASES 15 adverse reactions to cisplatin Ann-Marie Roche 22 October 2014 An introduction to indexing
- 16. ADVERSE REACTIONS TO CISPLATIN IN-DEPTH DRUG INDEXING 16 Ann-Marie Roche 22 October 2014 An introduction to indexing
- 17. DEFINITIONS OF ADVERSE EVENTS ON EMBASE AND MEDLINE 17 Embase first 4 of >100 terms PubMed / MEDLINE "chemicals and drugs category/adverse effects"[MeSH Terms] NOT ("chemicals and drugs category/toxicity"[MeSH Terms] OR "chemicals and drugs category/poisoning"[MeSH Terms]) Ann-Marie Roche 22 October 2014 An introduction to indexing Search using: Search using: "chemicals and drugs”/exp/dd_ae only in humans
- 18. 18 Adverse reactions to cisplatin EMBASE VS MEDLINE Ann-Marie Roche 22 October 2014 An introduction to indexing Embase
- 19. FINDING NEW DRUGS 19 Ref: http://www.news-sentinel.com/apps/pbcs.dll/article?AID=/20121115/NEWS/ 121119726/-1/LIVING Ann-Marie Roche 22 October 2014 An introduction to indexing
- 20. FINDING NEW DRUGS STEP 1: IDENTIFYING THE DRUG CATEGORY 20 Ann-Marie Roche 22 October 2014 An introduction to indexing
- 21. FINDING NEW DRUGS STEP 2: SEARCH USING THE DRUG CATEGORY 21 Change /exp to /de and add ‘unclassified drug’ (see notes) Ann-Marie Roche 22 October 2014 An introduction to indexing
- 22. FINDING NEW DRUGS STEP 3: CANDIDATE TERMS NOT FOUND IN EMTREE 22 Ann-Marie Roche 22 October 2014 An introduction to indexing
- 23. FINDING NEW DRUGS IDENTIFYING TRADE NAMES AND MANUFACTURERS 23 From drug index for this article Ann-Marie Roche 22 October 2014 An introduction to indexing
- 24. FINDING NEW DRUGS STEP 4: MORE INFORMATION ON TRADE NAMES AND LAB CODES 24 Ann-Marie Roche 22 October 2014 An introduction to indexing
- 25. BACK-POSTING? 25 Emtree is now updated 3x each year Terms added and changed are listed: http://www.embase.com/info/what-is-embase/ emtree New terms backposted to past years: a) if indexed earlier as candidate terms b) if previous PTs are assigned as synonyms Ann-Marie Roche 22 October 2014 An introduction to indexing
- 26. BACK-POSTING? 26 Ann-Marie Roche 22 October 2014 An introduction to indexing
- 27. SEARCHING FOR MEDICAL DEVICES NEW TREE STRUCTURE IN 2013 AND UPDATED IN 2014 27 Ann-Marie Roche 22 October 2014 An introduction to indexing
- 28. SEARCHING FOR MEDICAL DEVICES USING FILTERS TO SEARCH FOR TRADE NAMES AND COMPLICATIONS 28 Ann-Marie Roche 22 October 2014 An introduction to indexing
- 29. SEARCHING FOR EVIDENCE: STUDY TYPES AND TOPIC TERMS 29 From Emtree facet “Types of article or study” Include many more terms than check tags Now include “Topic terms” (from 2011) Topic terms: 10 terms ending with (topic) Topic terms were introduced in 2011 to differentiate between study types, indexed when the article IS the primary report for an RCT (for example), and articles in which that term is only a topic that is discussed. Ann-Marie Roche 22 October 2014 An introduction to indexing
- 30. MEDLINE RECORDS IN EMBASE 30 Over 9m records in Embase are licensed from NLM They currently come from over 2500 active journals … distributed over all years (1940 – present) 280,000 recs /yr 1974 Ann-Marie Roche 22 October 2014 An introduction to indexing
- 31. INDEXING PRINCIPLES 31 1. TRANSLATE To bring the semantic richness of medical terminology within your grasp: mapping many synonyms to a single (natural language) preferred terminology 2. EXPAND To expose and summarize the information in biomedical articles beyond title and abstract: discovering in-depth data about drugs, diseases and medical devices 3. FOCUS To identify the key concepts hidden within those articles – what they are really about – providing you with a toolkit to find answers beginning with comprehensive searches Ann-Marie Roche 22 October 2014 An introduction to indexing
- 32. THANK YOU ANY QUESTIONS? 32 Ann-Marie Roche 22 October 2014 An introduction to indexing
- 33. 33 AND FOR MORE INFORMATION … PLEASE FILL IN THE SURVEY WHICH WILL POP UP AT THE END OF THE WEBINAR. For more information and questions please use Help in Embase, where you may also find all training and support materials and our full webinar schedule. Our next Embase webinar is on November 26 and will focus on drug safety and device post-surveillance searching. We hope to have a special external guest also. The slides and recording will be shared within 24 hours. THANK YOU and SEE YOU NEXT TIME! Ann-Marie Roche 22 October 2014 An introduction to indexing
Editor's Notes
- First of all, I will show you how we index a typical article. This is an indexed article in Embase, with the concepts highlighted that in one way or another are represented in the Embase indexing. The concepts on this page come from the title and abstract …
- … but if you look further into the article, for example the Methods section, you see there are quite a few index concepts that we pick up here as well …
- And from the heart of the article, from tables as well as text, and from figures as well, our indexers identify important information that we think is important to index, such as (here) information about adverse drug events. In general, Embase indexers are seeking to identify important original information that is presented in the article, rather than hypotheses or ideas that might be mentioned in the discussion.
- For this article, the indexing process resulted in all the terms shown here, divided as you see into Drug terms, Disease terms, Other terms and Additional information. At the right hand side of each of the blue bars you can “open” the drug and disease terms, which is what I will show you next.
- Here first of all is the opened drug indexing. What you see is that each of the drug terms, here identified in the light blue bars, is qualified by a number of other terms. We call these subheadings, which may be “key subheadings” or “other subheadings”. Key subheadings have additional information shown in the middle column, which we call triple links. I’ll be showing more examples of this shortly.
- Here is the corresponding disease indexing. In this case it is quite lengthy, because each of the so-called disease terms is actually a side effect of one or more drug terms.
- In order to accurately and consistently index every article in Embase, our indexers use controlled vocabulary or a thesaurus called Emtree. You can see that alongside the structural aspects shown here on the left, Emtree has a very strong focus on drugs and chemicals. In fact more than 50% of the 60,000 or so terms in Emtree which we use for indexing – and which we call Preferred Terms – are drugs and chemicals. We have a very active policy to identify new drugs, and include in Emtree ALL generic names for drugs registered with various agencies, as well as New Drug Approvals registered with the FDA and EMA (European Medicines Agency). And as you can see on the right, we ensure that Emtree is updated 3x a year, including many new terms identified via our candidate terms procedure. Typically, well over 1,000 new Preferred terms are added each year to Emtree. [Click] ... Last year, we focused especially on medical devices terminology., as I will show you in a moment in more detail. We will look at backposting in more detail later.
- Top selling drugs in 2013 compared. The trade name was searched in Quick Search in Embase (mapped to Emtree term) and from the search box in Pubmed.
- You will find Emtree under ‘Browse’ in Embase. Click on ‘Browse by facet’ to get a picture of the structure. Each major branch has many, many sub-branches and you can keep clicking to get to more specific terms, such as a specific drug used to treat a specific condition or target in the body.
- Click on ‘Find term’ to more quickly get to a specific term. Here we looked for cisplatin. Click on ‘Take this query to Drug Search’ to further search for this drug and add filters and subheadings.
- Here we are searching for all adverse events reported for cisplatin in Embase.
- We can further refine from the search results page by clicking on the ‘Disease’ filter for example.
- Clicking on ‘Index terms’ in a specific article, we can find even deeper information, such as the specific side effects cited in this article for cisplatin. The indexers make a link between the drug, specific concepts such as adverse events and the disease, in this case the disease is the side effect.
- So let’s look at an example of how this might work. … and let’s suppose you are interested in developing new drugs for cystic fibrosis In this example, I am imagining that you found an article which mentions the treatment of cystic fibrosis with a new drug: kalydeco, a chloride channel stimulator. This might make you wonder what other similar drugs might be under development.
- In Emtree, you can quickly identify kalydeco as a synonym of ivacaftor Try looking for kalydeco in Quick Search. Even here you are prompted with what we call the ‘preferred term’ or Emtree term. Why is it the preferred Ivacaftor was added to Emtree in 2011, and is listed as a “chloride channel stimulating agents” So are there similar drugs under development in this category for treating cystic fibrosis? Even if they are not yet listed in Emtree, you can easily find them … Here’s how you do it ! First of all, you can search the entire category by clicking on the link indicated by the arrow.
- The result is shown here: this explosion search with /exp captures all the articles in the entire category. What you can now do is to edit the search to retrieve only records indexed with the category name itself To do that, you change the explosion to an exact search using /de Why should you do this? It’s because Embase indexers index using the most specific terms in Emtree. But if the terms they want to index are not yet covered in Emtree, they index the next best thing: its category. In this case, that is “ion transport affecting agent” As you can see, this already brings the number of results down. Of course, the indexer also indexes the new drug as a candidate term But as we don’t know what that is, we can’t search it directly. Fortunately there is a way around this. When he indexes a candidate drug term, there is one more thing the indexer has to do. He also indexes the term “unclassified drug” to indicate that he has assigned a candidate term. The first result looks quite promising, so let’s look at the index. As you can see, quite a few drug names are listed, including ivacaftor, the drug we started with. If you click on this (ivacaftor), you get more information about why it has been indexed in this article. As I mentioned before, the kind of indexing we see here is called “triple indexing”, because the subheading links two other terms … … in this case the triples are a drug linked to two other drugs, and a drug linked to a disease. You can’t actually search on triples yet, but you can see in the actual results what is linked with what, as here. Although you can’t see which drugs are the candidate terms here, it’s quite likely that one or more of the lab codes is in fact a candidate term. For example, if you click on the symbol next to “n6022” you can check whether the drug is in Emtree.
- In this case, ‘n 6022’ is not recognised by Emtree, so it must have been a candidate term
- In a similar article, the trade names, or lab codes, are also indexed separately, together with their manufacturers. The indexing rule is, that all these trade names are also searchable in the descriptor field as drugs. (xx) First of all, the codes highlighted in the red box were all indexed without any change as drug terms in this article. (you can see this by comparing the terms with the drug index at the bottom of the slide). This means they are either Emtree preferred terms in their own right, or candidate drug terms (like vx 661). (xx) However, the two lab codes on the right were don’t seem to have been indexed as drug terms. So what are they?
- A quick check in Emtree (now searching with the letters vx) shows that they are in fact the codes for ivacaftor and lumacaftor What happened in both cases is that the codes were mapped to their generic names; and it is the generic names that appear in the index.
- Emtree is now updated 3 times each year - you can find lists of added and changed terms at the URL shown on this slide. When we make these updates, we also reload Embase.com to update the indexing of older records whose indexing has changed. We call this backposting. (**) using the example we searched on earlier, we can see in Emtree that ivacaftor was introduced to Emtree in 2011
- However, if you search on ivacaftor you can find records that are indexed with this term as early as 2007. These earlier records have been backposted, and if you look at their indexes they will indeed display the current term, ivacaftor. The value of this to you as a searcher is that you don’t need to worry about name changes in Emtree. You can confidently search using the current version of Emtree, knowing that you will not miss any records that were indexed slightly differently in the past – they will have been backposted.
- Focus on prostheses and orthoses, getting to hip prosthesis.
- Embase check tags include a group of study types, such as “major clinical study” and “randomized controlled trial”. Another way of finding study types is to use the Filters at the left hand side of the results page, which I mentioned a few moments ago. (**) All of the study types mentioned here for one particular search are taken from the Emtree facet on “Types of article or study” (**) This is a rich source of terms that you can use to filter your search, and it now includes 10 so-called topic terms shown here, that I described last month in an Embase webinar on Evidence Based Medicine. If you want to follow up on this, you can access those slides via the Embase info site. This definition of topic terms, by the way, mirrors the definitions of similar terms which the NLM uses to index MEDLINE.
- The last topic I want to address here is the indexing of MEDLINE records on Embase. As you can see here, almost 9 million records on Embase.com are licensed from NLM. You can access them using the search shown here, where the records deduplicated against Embase and Embase Classic are NOT-ed out. (**) These records are spread over all the years of Embase, including the early years before 1974 also covered by Embase Classic.
- But first, let’s take a high level view of what is happening here. Probably like all databases, Embase indexing serves three main roles: to translate (**), expand (**), and focus (**). What is specific to Embase is how we interpret each of these aspects. For example: Under the heading translation, what is special about Embase is the natural language terminology used for indexing, and the very large number of synonyms. expansion stands for the in-depth indexing of drugs, diseases and in fact also medical devices which is derived from the full text of the article and focus refers to the specific tools that Embase makes available to help you drill down to the articles you need.